Introduction: This study investigated the perceptions and practices of Australian health professionals in relation to the use of functional capacity evaluations (FCE’s). Methods: A quantitative cross-sectional study design was used to survey health professionals who conduct FCE’s and who were working for one of 219 rehabilitation providers in NSW, Australia. Seventy seven returned surveys were eligible for inclusion. Results: Eleven different FCE’s were being utilised with many health professionals using more than one FCE. The most commonly used FCE was non-standardised (56%, n = 43) followed by 52% (n = 40) using the Workhab, and 18% (n = 14) using Valpar. Both non-standardised and standardised assessments were being used by 90% (n = 69) of respondents. Health professionals reported using all or parts of the FCE, and indicated identical FCE’s are not always conducted, with adaptation of the FCE, due to client injury (82%, n = 62) and job (80%, n = 43) occurring. About 60% of respondents had no choice in the type of FCE they conducted, and of the 40% with a choice, this was not influenced by other stakeholders in the process. Accreditation and training, characteristics of assessment tasks, standardisation, reliability, cost, length and flexibility were all identified as factors affecting the selection of an FCE. Conclusions: This study demonstrated that health professionals in NSW Australia, are not routinely using standardised tools for FCE’s. Health professional perceptions suggest accreditation, training and the characteristics of the FCE were important factors in FCE selection. In practice, participants tended to use parts of an FCE rather than the whole FCE. Adaptation of FCE’s was common, due to client injury and specific job requirements.